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Genetic basis of negative heterosis for growth traits in chickens revealed by genome-wide gene expression pattern analysis

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Journal of Animal Science and biotechnology 2021年第4期12卷 1267-1280页

作者： Chunning Mai Chaoliang Wen Zhiyuan Xu Guiyun Xu Sirui Chen Jiangxia Zheng Congjiao Sun Ning Yang National Engineering laboratory for Animal Breeding and Key laboratory of Animal Genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsChina Agricultural UniversityBeijing 100193China

Background:Heterosis is an important biological phenomenon that has been extensively utilized in agricultural ***,negative heterosis is also pervasively observed in nature,which can cause unfavorable impacts on production *** with systematic studies of positive heterosis,the phenomenon of negative heterosis has been largely ignored in genetic studies and breeding programs,and the genetic mechanism of this phenomenon has not been thoroughly elucidated to ***,we used chickens,the most common agricultural animals worldwide,to determine the genetic and molecular mechanisms of negative ***:We performed reciprocal crossing experiments with two distinct chicken lines and found that the body weight presented widely negative heterosis in the early growth of *** heterosis of carcass traits was more common than positive heterosis,especially breast muscle mass,which was over−40%in reciprocal ***-wide gene expression pattern analyses of breast muscle tissues revealed that nonadditivity,including dominance and overdominace,was the major gene inheritance *** genes,including a substantial number of genes encoding ATPase and NADH dehydrogenase,accounted for more than 68%of differentially expressed genes in reciprocal crosses(4257 of 5587 and 3617 of 5243,respectively).Moreover,nonadditive genes were significantly associated with the biological process of oxidative phosphorylation,which is the major metabolic pathway for energy release and animal growth and *** detection of ATP content and ATPase activity for purebred and crossbred progenies further confirmed that chickens with lower muscle yield had lower ATP concentrations but higher hydrolysis activity,which supported the important role of oxidative phosphorylation in negative heterosis for growth traits in ***:These findings revealed that nonadditive genes and their related oxidative phosphorylation were the m

关键词： Chicken Growth Gene expression patterns Heterosis Oxidative phosphorylation

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The outpost against cancer:universal cancer only markers

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Cancer Biology & Medicine 2023年第11期20卷 806-815页

作者： Chengchen Qian Xiaolong Zou Wei Li Yinshan Li Wenqiang Yu Shanghai Epiprobe biotechnology Co. LtdShanghai 200233China Department of General Surgery the First Affiliated Hospital of Harbin Medical UniversityHarbin 150001China Shandong Epiprobe Medical laboratory Co. LtdHeze 274108China People's Hospital of Ningxia Hui Autonomous Region Ningxia Medical UniversityYinchuan 750002China Shanghai Public Health Clinical Center&Department of General Surgery Huashan Hospital&Cancer Metastasis Institute&Laboratory of RNA EpigeneticsInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai 200032China

Cancer is the leading cause of death *** detection of cancer can lower the mortality of all types of cancer;however,effective early-detection biomarkers are lacking for most types of *** methylation has always been a major target of interest because DNA methylation usually occurs before other detectable genetic *** investigating the common features of cancer using a novel guide positioning sequencing for DNA methylation,a series of universal cancer only markers(UCOMs)have emerged as strong candidates for effective and accurate early detection of *** the clinical value of current cancer biomarkers is diminished by low sensitivity and/or low specificity,the unique characteristics of UCOMs ensure clinically meaningful *** of the clinical potential of UCOMs in lung,cervical,endometrial,and urothelial cancers further supports the application of UCOMs in multiple cancer types and various clinical *** fact,the applications of UCOMs are currently under active investigation with further evaluation in the early detection of cancer,auxiliary diagnosis,treatment efficacy,and recurrence *** molecular mechanisms by which UCOMs detect cancers are the next important topics to be *** application of UCOMs in real-world scenarios also requires implementation and refinement.

关键词： Cancer detection cancer screening DNA methylation cancer epigenetics cancer biomarkers

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Modeling and predicting the activities of trans-acting splicing factors with machining learning

Modeling and predicting the activities of trans-acting splic...

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中国生物化学与分子生物学会第十二届全国会员代表大会暨2018年全国学术会议

作者： Miaowei Mao Yue Hu Yun Yang Yajie Qian Huanhuan Wei Wei Fan Yi Yang Xiaoling Li Zefeng Wang CAS Key laboratory of Computational Biology CAS-MPG Partner Institute for Computational BiologyShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesCAS Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences Synthetic Biology and biotechnology laboratory State Key Laboratory of Bioreactor EngineeringSchool of PharmacyEast China University of Science and Technology Signal Transduction laboratory National Institute of Environmental Health Sciences

Alternative splicing(AS) is generally regulated by trans-splicing factors that specifically bind to cis-elements in *** genome encodes ～1500 RNA binding proteins(RBPs) that potentially regulate AS,yet their function remain largely *** explore their potential activities,we fused the putative functional domains of RBPs to a sequence-specific RNAbinding domain,and systemically analyzed how these engineered factors affect *** discovered that ～80% of low complexity domains in endogenous RBPs displayed distinct context-dependent activities in regulating splicing,indicating that AS is under more extensive regulation than previously *** developed a machine learning approach classify and predict the activities of RBPs based on their sequence compositions,and further validated this model using endogenous RBPs and synthetic *** results represent a systematic inspection,modeling,prediction and validation of how RBP sequences affect their activities in controlling splicing,paving the way for de novo engineering of artificial splicing factors.

关键词： Alternative splicing Splicing factors Machine learning RNA binding domains Protein engineering Protein activity prediction

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Contact Mechanism of the Ag-doped Trimolybdate Nanowire as An Antimicrobial Agent

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Nano-Micro Letters 2012年第4期4卷 228-234页

作者： Yujie Jiang Jian Gang Sheng-Yong Xu Key laboratory for the Physics and Chemistry of Nanodevices and Department of Electronics Peking University

Antibacterial Ag-agents are intensively applied as broad spectrum, high-stability, high-efficiency and high-safety inorganic antibacterial agents. We have developed a new kind of antibacterial Ag-agent, namely Ag_2-x(NH_4)xMo_3O_(10) ·3H_2O nanowires(NWs). Carrying Ag atoms in the lattice and Ag-rich nanoparticles on the surface, the Ag-doped NWs show strong antibacterial effects for a variety of bacteria including ***, Staphylococcus aureus, Candida albicans and Aspergil lus niger. By performing systematic comparison experiments, we have proven that the main antibacterial effects are neither resulted from the tiny amount of Ag+ions released from the Ag-doped NWs in aqueous solutions, nor resulted from Ag-rich nanoparticles of fragments of the NWs when they are slowly dissolved in the Martin broth. Instead, the effects are mainly resulted from a contact mechanism, under which, the Ag-doped NWs need to be physically in contact with the bacteria to be eliminated. This is a novel phenomenon observed in the interactions between nanomaterials and live cells, which is worthy of further investigation at the molecular scale. As the Ag-doped NWs are not dissolved in pure water or weak acids, one may find practical antibacterial applications in textile industry and food storage industry for these unique nanomaterials.

关键词： Antibacterial agent Antibacterial Ag-agent Silver ions Silver-rich nanoparticles Silver-doped trimolybdate nanowire Bio-safety of nanomaterials Contact mechanism

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Trends in insulin resistance:insights into mechanisms and therapeutic strategy

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Signal Transduction and Targeted Therapy 2022年第8期7卷 2762-2786页

作者： Mengwei Li Xiaowei Chi Ying Wang Sarra Setrerrahmane Wenwei Xie Hanmei Xu The Engineering Research Center of Synthetic Peptide Drug Discovery and Evaluation of Jiangsu Province China Pharmaceutical UniversityNanjing 210009China State Key laboratory of Natural Medicines Ministry of EducationChina Pharmaceutical UniversityNanjing 210009China Development Center for Medical Science&Technology National Health Commission of the People’s Republic of China 100044 BeijingChina NANJING ANJI biotechnology CO.LTD Nanjing 210033China

The centenary of insulin discovery represents an important opportunity to transform diabetes from a fatal diagnosis into a medically manageable chronic *** is a key peptide hormone and mediates the systemic glucose metabolism in different *** resistance(IR)is a disordered biological response for insulin stimulation through the disruption of different molecular pathways in target *** conditions and genetic factors have been implicated in *** genetic and biochemical studies suggest that the dysregulated metabolic mediators released by adipose tissue including adipokines,cytokines,chemokines,excess lipids and toxic lipid metabolites promote IR in other *** is associated with several groups of abnormal syndromes that include obesity,diabetes,metabolic dysfunction-associated fatty liver disease(MAFLD),cardiovascular disease,polycystic ovary syndrome(PCOS),and other *** no medication is specifically approved to treat IR,we summarized the lifestyle changes and pharmacological medications that have been used as efficient intervention to improve insulin ***,the systematic discussion of complex mechanism will help to identify potential new targets and treat the closely associated metabolic syndrome of IR.

关键词： metabolism stimulation diagnosis

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Electrocardiogram-based artificial intelligence for the diagnosis of heart failure:a systematic review and meta-analysis

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Journal of Geriatric Cardiology 2022年第12期19卷 970-980,1011-1015页

作者： Xin-Mu LI Xin-Yi GAO Gary Tse Shen-Da HONG Kang-Yin CHEN Guang-Ping LI Tong LIU Tianjin Key laboratory of Ionic-molecular Function of Cardiovascular Disease Department of CardiologyTianjin Institute of CardiologySecond Hospital of Tianjin Medical UniversityTianjinChina Kent and Medway Medical School CanterburyUnited Kingdom National Institute of Health Data Science at Peking University Peking UniversityBeijingChina Institute of Medical Technology Peking University Health Science CenterBeijingChina

BACKGROUND The electrocardiogram(ECG)is an inexpensive and easily accessible investigation for the diagnosis of cardiovascular diseases including heart failure(HF).The application of artificial intelligence(AI)has contributed to clinical practice in terms of aiding diagnosis,prognosis,risk stratification and guiding clinical *** aim of this study is to systematically review and perform a meta-analysis of published studies on the application of AI for HF detection based on the *** We searched Embase,PubMed and Web of Science databases to identify literature using AI for HF detection based on ECG *** quality of included studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2(QUADAS-2)***-effects models were used for calculating the effect estimates and hierarchical receiver operating characteristic curves were *** analysis was *** and the risk of bias were also *** A total of 11 studies including 104,737 subjects were *** area under the curve for HF diagnosis was 0.986,with a corresponding pooled sensitivity of 0.95(95%CI:0.86–0.98),specificity of 0.98(95%CI:0.95–0.99)and diagnostic odds ratio of 831.51(95%CI:127.85–5407.74).In the patient selection domain of QUADAS-2,eight studies were designated as high *** According to the available evidence,the incorporation of AI can aid the diagnosis of ***,there is heterogeneity among machine learning algorithms and improvements are required in terms of quality and study design.

关键词： diagnosis assessed specificity

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A systematic investigation of high harmonic generation using mid-infrared driving laser pulses

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Science China(Physics,Mechanics & Astronomy) 2010年第6期53卷 1054-1059页

作者： YAO JinPing 1,2 ,XIONG Hui 1 ,XU Han 1 ,FU YuXi 1,2 ,ZENG Bin 1,2 ,CHU Wei 1,2 ,CHENG Ya 1 ,XU ZhiZhan 1 ,LIU XiaoJun 3 & CHEN Jing 4,5 1 State Key laboratory of High Field Laser Physics,Shanghai Institute of Optics and Fine Mechanics,Chinese Academy of Sciences,Shanghai 201800,China 2 Graduate University of Chinese Academy of Sciences,Beijing 100049,China 3 State Key laboratory of Magnetic Resonance and Atomic and molecular Physics,Wuhan Institute of Physics and Mathematics,Chinese Academy of Sciences,Wuhan 430071,China 4 Institute of Applied Physics and Computational Mathematics,Beijing 100088,China 5 Center for Applied Physics and Technology,Peking University,Beijing 100084,China State Key laboratory of High Field Laser Physics Shanghai Institute of Optics and Fine Mechanics Chinese Academy of Sciences Shanghai China Graduate University of Chinese Academy of Sciences Beijing China State Key laboratory of Magnetic Resonance and Atomic and molecular Physics Wuhan Institute of Physics and Mathematics Chinese Academy of Sciences Wuhan China Institute of Applied Physics and Computational Mathematics Beijing China Center for Applied Physics and Technology Peking University Beijing China

We report on a systematic investigation of the influences of gas pressure,focal position and focusing geometry on high harmonic generation by use of mid-infrared femtosecond laser pulses. We also discuss the spatial characteristics of harmonics under different focusing conditions. By optimizing the parameters,we experimentally observed the generation of 1 kHz,low divergence coherent X-ray beams in the water-window region.

关键词： mid-infrared laser pulses high harmonic generation water window

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A systematic investigation of Complement and Coagulation-Related Protein in Autism Spectrum Disorder Using Multiple Reaction Monitoring Technology

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Neuroscience Bulletin 2023年第11期39卷 1623-1637页

作者： Xueshan Cao Xiaoxiao Tang Chengyun Feng Jing Lin Huajie Zhang Qiong Liu Qihong Zheng Hongbin Zhuang Xukun Liu Haiying Li Naseer Ullah Khan Liming She College of Life Science and Oceanography Shenzhen UniversityShenzhen518060China College of Physics and Optoelectronics Engineering Shenzhen UniversityShenzhen518060China Maternal and Child Health Hospital of Baoan Shenzhen518100China Department of Endocrinology Guiyang First People’s HospitalGuiyang550002China Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions Shenzhen518055China Shenzhen Key laboratory of Marine biotechnology and Ecology Shenzhen518060China

Autism spectrum disorder(ASD)is one of the common neurodevelopmental disorders in *** etiology and pathogenesis are poorly *** studies have suggested potential changes in the complement and coagulation pathways in individuals with *** this study,using multiple reactions monitoring proteomic technology,16 of the 33 proteins involved in this pathway were identified as differentially-expressed proteins in plasma between children with ASD and *** them,CFHR3,C4BPB,C4BPA,CFH,C9,SERPIND1,C8A,F9,and F11 were found to be altered in the plasma of children with ASD for the first ***1 expression was positively correlated with the CARS *** the machine learning method,we obtained a panel composed of 12 differentially-expressed proteins with diagnostic potential for *** also reviewed the proteins changed in this pathway in the brain and blood of patients with *** complement and coagulation pathways may be activated in the peripheral blood of children with ASD and play a key role in the pathogenesis of ASD.

关键词： pathogenesis children complement

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Transcriptomic study of the red palm weevil Rhynchophorus ferrugineus embryogenesis

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Insect Science 2015年第1期22卷 65-82页

作者： An Yin Linlin Pan Xiaowei Zhang Lei Wang Yuxin Yin Shangang Jia Wanfei Liu Chengqi Xin Kan Liu Xiaoguang Yu Gaoyuan Sun Khalid AI-hudaib Son qnian Hu Ibrahim S. AI-Mssallem Jun Yu joint Center for Genomics Research (JCGR) King Abdulaziz City for Science and Technology (KACST) and Chinese Academy ofSciences (CAS) Riyadh Kingdom of Saudi Arabia CAS Key laboratory of Genome Sciences and Information Beijing Institute ofGenomics Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China plant ProtectionDepartment Department of biotechnology College of Agriculture and Food Sciences King Faisal University AI-Hssa HofufKingdom of Saudi Arabia

The red palm weevil （RPW）, Rhynchophorus ferrugineus （Coleoptera： Cur- culionidae）, is an invasive, concealed and destructive tissue borer, and it becomes a lethal pest of the palm family of plants and has been reported to attack 20 palm species around the globe. Here we report a systematic transcriptomic study on embryogenesis of RPW, where we analyze the transcriptomes across five developmental stages of RPW embryogenesis, involving four embryonic stages （El, E2, E3 and E4） and one larval stage （L1）. Using the RNA-seq and next-generation platforms, we generated 80 to 91 million reads for each library and assemble 22 532 genes that are expressed at different embryonic stages. Among the total transcripts from the five embryonic development stages, we found that 30.45 % are differentially expressed, 10.10 % show stage-specificity and even a larger fraction, 62.88 %, exhibit constitutive expression in all the stages. We also analyzes the expression dynamics of several conserved signaling pathways （such as Hedgehog, JAK-STAT, Notch, TGF-β, Ras/MAPK and Writ）, as well as key developmental genes, including those related to apoptosis, axis formation, Hox complex, neurogenesis and segmentation. The datasets provide an essential resource for gene annotation and RPW functional genomics, including studies by using tools and concepts from multiple disciplines, such as development, physiology, biochemistry, molecular biology and genetics.

关键词： insect embryogenesis red palm weevil Rhynchophorusferrugineus RNAseq signaling pathways transcriptome

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investigation of Methylation Profiles of TP53, Caspase 9, Caspase 8, Caspase 3 Genes Treated with DNA Methyl Transferase Inhibitor (DNMTi) Zebularine (ZEB) and Caffeic Acid Phenethyl Ester (CAPE) on MCF-7 and MDA-MB-231 Breast Cancer Cell Lines

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Journal of Cancer Therapy 2019年第1期10卷 69-85页

作者： Onur Eroglu Esin Guvenir Celik Hacer Kaya Merve Celen Mustafa Karabicici Elif Karacoban Department of molecular Biology and Genetics Faculty of Science and Letters Bilecik Seyh Edebali University Bilecik Turkey biotechnology Research and Application Center Bilecik Seyh Edebali University Bilecik Turkey Vocational School of Medical Services Program of Medical Laboratory Techniques Bilecik Seyh Edebali University Bilecik Turkey Izmir Biomedicine and Genome Center Dokuz Eylul University Izmir Turkey

Purpose: MCF-7 (ER+, WTP53) and MDA-MB-231 (ER Met, Mutant P53) Caffeic Acid Phenethyl Ester (CAPE) and DNA Methyl Transferase Inhibitor (DNMTi) in breast cancer cell lines of Zebularine (ZEB) single and combined application of TP53, caspase-9, caspase 8 and caspase-3 genes as a result of the use of single and combined drug methylation profiles are aimed to be evaluated by specific PCR method. Material-Metods: In the MCF-7 and MDA-MB-231 breast cancer cell lines, MTT test and survival analysis were performed as a result of single and combined application of CAPE and Zebularine and Methylation Specific PCR was performed to examine the methylation of caspase-3, caspase-8, caspase-9 and TP53 genes. Results: According to the results of 24-hour drug administration, the IC50 for the MCF-7 cell line was determined as 200 μM, for CAPE 40 μM and for the combined values of 50 μM ZEB + 5 μM CAPE. The effects of caspase-3, caspase-8, caspase-9 and TP53 genes on the methylation level of ZEB, CAPE and ZEB + CAPE drug combination were determined by using bisulfite modified DNAs in MCF-7 and MDA-MB-231 cell lines. Discussion: In the MCF-7 cell line, the 120 μM ZEB viability rate was 51%, and the viability of 80 μM ZEB MDA-MB-231 breast cancer cells decreased by 59.7%. After 20 μM CAPE, viability in MCF-7 cells decreased by 31% in 120 μM CAPE and MDA-MB-231 cells decreased by 41%. The viability with 40 μM CAPE decreased by 19% in MDA-MB-231 cells. It was found that 20 μM CAPE concentration was associated with TP53 methylation in MCF-7 cell lines. The 80 μM ZEB concentration was found to be closely related to the unmethylated status of the TP53 gene. These results obtained with 50 μM ZEB + 5 μM CAPE application were found to be related to the methylated-unmetylated status of the TP53 gene in half (50%). For the caspase-9 gene of MDA-MB-231 cells, 80 μM ZEB concentration was found to be associated with unmetylated status. The effective use of drugs with low concentrations of the drug

关键词： MCF-7 MDA-MB-231 Zebularine CAPE Breast Cancer Methylation

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